Microbial Ecology
Gk. oikos "house, dwelling
place, habitation
Chapter 30
The emergence of the
science of ecology is easily
summed up:
EVERYTHING IS
CONNECTED.
Bill McKibben
.Holistic vs reductionist approaches
Principles of Microbial Ecology
Ecology is study of relationships of
organisms to each other and environment
Organisms in given area are termed a
community
Living communities interact with each other
and non-living , abiotic, environment
Interactions include competition, symbiosis,
decomposition,
This interaction forms an ECOSYSTEM
Ecology is study of relationships of organisms to
each other and environment
Organisms in given area are termed a community
LIVING
Non -LIVING
(cells, organisms
(abiotic)
Communities etc.
Together comprise an ECOSYSTEM
Principles of Microbial Ecology
Major ecosystems include
Oceans, rivers, lakes, deserts, marshes, grasslands,
forests and tundra
Each ecosystem contains certain organisms and
characteristic physical conditions
Region of earth inhabited by living organisms
termed biosphere
Ecosystems vary within biosphere in biodiversity
and biomass
Biodiversity = number of species present and
evenness of distribution
Biomass = weight of all organisms present
Accelerated studies in Biodiversity
Tapei 101 - 1670 ft
Breakdown by mixed cultures of
microalaged, Sphingomonas GY2B and
Burkholderia cepacia GS3C,
Alcanivorax and Pseudomonas
Tang et al, 2010
Why study microbes and their diversity?
Microbes are root of all life; diversity fuels evolution;
most microbes are not isolated
Microbial DIVERSITY represents most of the
biodiversity in the biosphere
High abundance in most habitats - ~ 10 9 eubacteria
per liter seawater
Serial endosymbioses theory - ancestor of
multicellular life
Medicine, human health, effects on the environment
Some Statistics.
prokaryotic cell density in aquatic environments
continental shelf and upper 200 m of open ocean =
AVG 5 X 10 5 cells/ ml mostly cyanobacteria (4 X 104) ;
but up to 10 7 bacteria/ ml
Total carbon of prokaryotes on earth is enormous -
60 100% of the total carbon found in plants.
10 30 microbes estimated worldwide
50 bacterial phyla, with only 50% composed
entirely of uncultured bacteria
Most bacterial diversity unexplored
10 30 microbes estimated worldwide
Open ocean: SAR 11 (Pelagibacter) represented
>25% of marine SAR 16S rRNA library
Terrestrial Habitats
Human interest in microbiology of the soil stems
from ability of microbes to synthesize a variety of
useful chemicals
500 different antibiotics substances produced by
Streptomyces species
geosmins give soil the musty odor
50 have useful application in medicine, agriculture and
industry
Soil microbes being tested for their ability to degrade
toxic chemicals
Other microbes - Clostridium, Azotobacter
Terrestrial Habitats
4000 different species per gram/soil
Top 6 inches of fertile soil may harbor > 2
tons of bacteria or fungi per acre
Large environmental fluctations and
gradients
Principles of Microbial Ecology
Microorganisms play major role in most
ecosystems
Role an organism plays in ecosystem is
termed ecological niche
Environment immediately surrounding
microorganism is termed microenvironment
Most relevant to that cell
Often difficult to identify and measure
Macro environment may be more easily measured and is
very different from microenvironment
Organisms MODIFY their environment
and visa versa
Normal flora defined as populations of microorganisms routinely found
growing on the body of healthy individual have specific niches on the body
or environment
Principles of Microbial
Ecology
Nutrient acquisition
Organisms are categorized
according to trophic level
Trophic = Feeding, or source
of food
Level is intimately related to
cycling of nutrients
Three general trophic levels
Primary producers
Consumers
Decomposers
Primary producers
Primary producers are autotrophs
Convert carbon dioxide to organic
materials
Include
Photoautotrophs
Plants
Algae
Cyanobacteria
Anoxygenic phototrophs
All use sunlight for energy
Chemoautotrophs
Oxidize inorganic
compounds for energy
Primary producers serve as food
source for consumers and
decomposers
Consumers
Consumers are heterotrophs
Rely on activities of primary
producers
Herbivores eat primary producers
Termed primary consumers
Carnivores consume herbivores
Termed secondary consumers
Carnivores that eat other
carnivores
Termed tertiary consumers
Chain of consumption is the food
chain
Interaction between food chains
called food webs
From
Thompsma
Principles of Microbial Ecology
Decomposers
Decomposers are heterotrophs that
digest remains of primary producers
and consumers
Partially decomposed organic matter
of other trophic levels termed detritus
Decomposers specialize in digestion
of complex material
Convert them into small molecules
Molecules more readily usable by
other organisms
Complete breakdown of organic
molecules to inorganic molecules is
termed mineralization
Principles of Microbial Ecology
Bacteria in low-nutrient environments
(oligotrophic)
These environments common in nature
Growth in these areas most often in form of biofilm
Not restricted to specific environments like lakes and streams
Organisms can also grow in distilled environments of hospital water
reservoirs
Microbes can extract amounts of nutrient absorbed by
water
Growth usually goes unnoticed
Can have serious consequences in hospitalized patients
Organisms that survive in low nutrient environments
often have highly efficient transport systems for nutrient
procurement
Principles of Microbial
Ecology
Microbial competition
and antagonism
Results of competition
evident among
organisms
Ability to compete is
generally related to rate
of growth
Organisms that
multiply faster yield
larger population and
use more nutrient
supply
Antagonism helps
determine make-up of
population -
Natural products
Bacteriocin produced by
certain species to kill
other strains
Form of chemical
antagonisms
Principles of Microbial Ecology
Microorganisms and environmental change
Environmental change often results in
alterations in a bacterial community
In order for organism to survive in new conditions it
must adapt to altered environment
In response to new stimuli microbes stop producing
enzymes that serve no purpose
Mutants within a population may remain in minority
in current population
Mutation may make organism well suited for new changed
environment
Biogeochemical Cycling and
Energy Flow
Biochemical cycles are cyclical paths that
elements take as they flow through living
and nonliving components of the
ecosystem
Living = biotic
Non-living = abiotic
Cycles are important
Allows ecosystem to sustain characteristic life
forms through recycling of elements
Carbon and nitrogen cycle important in the
recycling of environmental components
Biogeochemical Cycling and
Energy Flow
Nitrogen cycle
Consumers ingest plants and animals to fulfill
both their carbon, energy and nitrogen needs
Nitrogen is used solely to build biomass
Prokaryotes are more diverse in their use of
nitrogen compounds
Some use nitrite and nitrate as terminal
electron acceptors
Others use ammonium as and energy source
Biogeochemical Cycling and
Energy Flow
Sulfur oxidation
Hydrogen sulfide and elemental sulfur can
both serve as energy sources for certain
chemolithotrophs
Some bacteria oxidize these molecules to
sulfate
Hydrogen sulfide and elemental sulfur are
oxidized anaerobically by photosynthetic
green and purple sulfur bacteria
Use sunlight as energy but need reduced
molecules as source of electrons and reducing
power
Biogeochemical Cycling and
Energy Flow
Sulfur reduction
Under anaerobic conditions sulfate can be
used as terminal electron acceptor
Sulfur and sulfur-reducing bacteria and
archaea use sulfate in anaerobic respiration
Reducing sulfate to hydrogen sulfide
Principles of Microbial Ecology
Microbial communities
Microorganisms often grow in communities
attached to some solid surface at at air-water
interface
Usually grow in biofilms or microbial mats
Resident, established communities tend to
Inhibit newcomers
----> Competitive Exclusion
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Deep Sea Hydrothermal Vent Communities -black smokers
Deep sea, hydrothermal vents, are underwater springs that
occur near zones of sea floor spreading - here earth's crust
is very thin, seawater seeps in and is heated by magma
below the ocean floor and eject again through cracks in the
bottom. During contact with the hot rocks, the chemical
composition of the seawater is radically changed; The water
absorbs many minerals and some of its sulfate is reduced to
sulfide.
Vents occur at mid ocean ridges and back-arc basin spreading
ridges, continental margins in cold water sulfide and methane
seeps. Pacific vents have short life spans.
Other habitats that support symbioses sewage outfalls,
eelgrass beds, mangrove swamps, hypoxic ocean basins
all have in common with vents the presence of a redox
boundary where a source of reduced sulfur compounds is
found close to a source of oxygen.
VENTS: There is no obvious food
source, so unlike all other
photosynthetic communities,
vents are based primarily on bacterial
chemosynthesis fueled by sulfide
arising from the geothermal reduction
of sulfate. Chemolithoautotrophic
bacteria live on sulfide, a rich source of
energy and reducing power for free-
living and endosymbiotic bacteria
All of the tubeworm endosymbionts appear to be
close relatives of gamma subdivision. There is
congruence (agreement) between host and symbiont
branching trees (phylogenies), indicating common
ancestry for these symbioses, and subsequent
divergence/coevolution of symbionts with their respective
hosts over time.
Evolutionary separation of vent vs. seep
endosymbionts appears to have preceded
diversification of the tube worm hosts (Delong, 1998).
Vestimentiferan endosymbionts are probably
Horizontally transferred (taken up from the
environment and free living bacteria rather than
vertically passed on from parent to offspring),
since bacteria were not detected in eggs.
Biogeochemical Cycling and
Energy Flow
Phosphorus cycle and other cycles
Phosphorus is component of several
biological compounds
Most plants and microorganisms readily take
up phosphorus as orthophosphate
Assimilate it into biomass
In many aquatic habitats growth of primary
producers often limited by low concentrations
of phosphorus
Other elements such as iron, calcium, zinc,
magnesium, cobalt and mercury are also
cycled by microorganisms
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Marine
Total described marine species (1997) = 274,000
Deep sea area - >1000 m , covers 3 X 108 sq km of earth,
if 1 new species / sq km = 3 X 10 8 species., maybe 107 -
108 marine nematode species.
Approximately 65% of planet is covered by ocean greater
than 130 m in depth (approximate depth limit of continental
shelf); average depth of the ocean is ~13,000 ft.
prokaryotic cell density in aquatic environments
continental shelf and upper 200 m of open ocean = AVG 5
X 10 5 cells/ ml mostly cyanobacteria (4 X 104) ; but up to
10 7 bacteria/ ml
Tapei 101 - 1670 ft
Unexpected gene,
Proteorhodpopsin, found in
Shotgun libraries
Photorhodopsin is an integral membrane protein
composed of seven -helices that form a pocket that
encloses a single retinal chromophore (1, 4). The
light-sensitive properties of PR proteins are derived
from a covalent attachment of retinal to a lysine
residue at position 232 by means of a protonated
Schiff base linkage (7). The chromophore is activated
by the absorption of a photon of light and functions to
activate a biochemical cascade.
Retinal is a light-sensitive derivative of vitamin A, and
opsin is a protein molecule.
Aquatic Habitats
Deep lakes and oceans have characteristic zones
Zones influence distribution of microbial populations
Upper zone has sufficient light penetration to support photosynthetic
microorganisms
Organic material produced by these organisms descends and is
metabolized by heterotrophs
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Eutrophic Lakes
Aquatic Habitats
In oligotrophic waters growth of photosynthetic
organisms is limited due to lack of certain
nutrients
Eutrophic waters support robust multiplication of
photosynthetic organisms due to rich content of
nutrient
Activity of surface organisms produce nutrient
compounds for heterotrophic growth in lower levels
Heterotrophs consume oxygen during metabolism of
nutrient
Waters may become hypoxic
Leads to death of resident aquatic wildlife
Gulf of
Mexico
Dead Zone
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Aquatic Habitats
Marine environments
Range from deep sea to shallower coastal regions
Nutrients scarce in deep sea regions
Nutrients abundant in shallow coastal region
Seawater contains high salt concentration
Supports halophilic organisms
Ocean waters usually oligotrophic
Limits growth of microorganisms
Ecology of inshore areas not as stable as deep sea
Can be dramatically affected by nutrient-rich runoff
Consequence = populations of algae and cyanobacteria flourish
Oxygen is consumed and regions become hypoxic
Hypoxic regions termed dead zone